Train,Predict&Validate. Minresol vs Set_val.
Тренируемся на minresol, исключая общие цепи.
- Результаты на set_val, исключая общие цепи.
- Результаты на set_val, включая общие цепи.
- Результаты на minresol.
In [1]:
import sys
sys.path.insert(0, '../basic codes')
import class_magnesium_not_drop_na
from class_magnesium_not_drop_na import *
from matplotlib.backends.backend_pdf import PdfPages
import sys
from IPython.core.display import clear_output
def change_output(x):
clear_output()
sys.stdout.write(x)
sys.stdout.flush()
import xgboost as xgb
In [4]:
import importlib
importlib.reload(class_magnesium_not_drop_na)
from class_magnesium_not_drop_na import *
In [2]:
class Magnesium_validation(Magnesium):
def __init__(self, validation_file, drop_common = True, *args, **kwargs):
change_output('Loading data...')
super(Magnesium_validation, self).__init__(*args, **kwargs)
change_output('Loading validation data...')
self.validation_data = pd.read_table(validation_file).fillna(method = 'backfill', axis = 0)
if np.sum(self.validation_data.isnull().any(axis=1)) > 0:
self.validation_data.fillna(method = 'pad', axis = 0, inplace = True)
self.validation_data = self.validation_data[~(self.validation_data['chainlen']>1000)]
angles = ['p', 'phase-angle', 'e-z',
'tm', 'sszp', 'etap', 'etapp',
'splay', 'thetap', 'thetapp']
angles = np.ravel([[''.join([i,j]) for i in angles] for j in ['m2', 'm1', '', '1', '2']])
self.validation_data.drop(angles, axis=1)
self.data.drop(angles, axis=1)
if ('DSSR' in self.data.columns):
self.data.drop('DSSR', axis=1, inplace=True)
if ('DSSR' in self.validation_data.columns):
self.validation_data.drop('DSSR', axis=1, inplace=True)
change_output('Data loaded')
change_output('Data processing')
self.common_data = self.validation_data[self.validation_data['pdb_chain'].isin(self.data['pdb_chain'])]
self.data = self.data[~self.data['pdb_chain'].isin(self.common_data['pdb_chain'])]
if drop_common:
self.validation_data = self.validation_data[~self.validation_data['pdb_chain'].isin(self.common_data['pdb_chain'])]
self.x_test = np.matrix(self.validation_data[list(self.validation_data.columns)[1:-1]])
self.y_test = np.array(self.validation_data[list(self.validation_data.columns)[-1]])
self.data_numpy = np.matrix(self.data)
self.x = self.data_numpy[:, 1:-1]
self.y = np.array(self.data_numpy[:,-1].flatten().tolist()[0])
change_output("Data processed")
def train(self, n_splits):
change_output("Start training...")
self.trained_model_validation = self.model
x = self.x
y = self.y
sss = StratifiedShuffleSplit(n_splits = n_splits, test_size = 0.3, random_state = 0)
rus = RandomUnderSampler(ratio = 'auto', random_state=42)
splitted = sss.split(x, y)
iterator = tqdm_notebook(splitted, desc = "Splits", leave = True) if tqdm else splitted
for train_index, test_index in iterator:
x_train, y_train = rus.fit_sample(x[train_index], y[train_index])
self.trained_model_validation.fit(x_train, y_train)
if not os.path.isdir('trained_models'):
os.mkdir('trained_models')
model_name = '%s_depth=%d_leaves=%d_%s_validation'%(re.split("\.|\'", str(self.trained_model_validation.__class__))[-2],
self.trained_model_validation.__dict__['max_depth'],
self.trained_model_validation.__dict__['min_samples_leaf'],
self.filename)
with open("trained_models/"+model_name+".sav", 'wb') as file_to_save:
pickle.dump(self.trained_model_validation, file_to_save)
change_output("Trained")
return [x[test_index], y[test_index]]
def compute_validated(self, n_splits = 3):
x_test, y_test = self.train(n_splits)
data = self.predict(x = self.x_test, y = self.y_test, model=self.trained_model_validation)
self.show_plots(data['plots'])
plt.text(0.02, 0.5, 'Predict', fontsize=14)
data_train = self.predict(x = x_test, y = y_test, model=self.trained_model_validation)
self.show_plots(data_train['plots'])
plt.text(0.02, 0.5, 'Train', fontsize=14)
self.validation_data['prediction'] = data['prediction']
self.validation_data['probability'] = data['probability']
return data
Тренируемся на minresol
In [3]:
#fold = 'https://tikhonovapolly.files.wordpress.com/2017/09/'
fold = '../main_datasets/'
m_straight_without = Magnesium_validation('../main_datasets/set_val_A_7_new.csv', drop_common = True, file_ = "set_minresol_a_7_1000_new.csv", fold = fold,
model = RandomForestClassifier(n_estimators=200, n_jobs=-1, criterion='gini', max_depth = 39, min_samples_leaf = 1))
In [4]:
m_straight_without.train(n_splits=5);
Результаты на set_val, исключая совпадающие с трейном цепи.
In [38]:
fig = plt.figure(figsize = (20, 100))
fig.set_facecolor('white')
plt.subplots_adjust(hspace=0.3)
data_straight_without = m_straight_without.predict(x = m_straight_without.x_test,
y = m_straight_without.y_test,
model=m_straight_without.trained_model_validation)
n = np.unique(m_straight_without.validation_data['pdb_chain']).shape[0]//2+1
k = 0
fig.add_subplot(n,1, 1)
plot = data_straight_without['plots']['prob_density']
[eval(plot_string) for plot_string in plot]
plt.title('Probabiity Distributions. Validation \nPortion of sites - %.2f'%(np.sum(m_straight_without.y_test==1)/m_straight_without.y_test.shape[0]))
for i,chain in enumerate(np.unique(m_straight_without.validation_data['pdb_chain'])):
dataset = m_straight_without.validation_data[m_straight_without.validation_data['pdb_chain'] == chain]
x_test = np.matrix(dataset[list(m_straight_without.validation_data.columns)[1:-1]])
y_test = np.array(dataset[list(m_straight_without.validation_data.columns)[-1]])
if np.sum(y_test==1) > 0:
fig.add_subplot(n,2, i+3-k)
data = m_straight_without.predict(x = x_test,
y = y_test,
model=m_straight_without.trained_model_validation)
plot = data['plots']['prob_density']
[eval(plot_string) for plot_string in plot]
#m_straight_without.show_plots(plot)
plt.title('Probabiity Distributions. %s\nPortion of sites - %.2f'%(chain.title(), np.sum(y_test==1)/y_test.shape[0]))
else:
print("Chain %s has no sites. "%(chain))
k += 1
Результаты на set_val, включая совпадающие с трейном цепи.
In [18]:
m_straight_with = Magnesium_validation('../main_datasets/set_val_A_7_new.csv', drop_common = False, file_ = "set_minresol_a_7_1000_new.csv", fold = fold,
model = RandomForestClassifier(n_estimators=200, n_jobs=-1, criterion='gini', max_depth = 39, min_samples_leaf = 1))
m_straight_with.trained_model_validation = m_straight_without.trained_model_validation
fig = plt.figure(figsize = (20, 50))
fig.set_facecolor('white')
plt.subplots_adjust(hspace=0.3)
data_straight_with = m_straight_with.predict(x = m_straight_with.x_test,
y = m_straight_with.y_test,
model=m_straight_with.trained_model_validation)
n = np.unique(m_straight_with.common_data['pdb_chain']).shape[0]//2+2
k = 0
fig.add_subplot(n,1, 1)
plot = data_straight_with['plots']['prob_density']
[eval(plot_string) for plot_string in plot]
plt.title('Probabiity Distributions. Validation \nPortion of sites - %.2f'%(np.sum(m_straight_with.y_test==1)/m_straight_with.y_test.shape[0]))
for i,chain in enumerate(np.unique(m_straight_with.common_data['pdb_chain'])):
dataset = m_straight_with.common_data[m_straight_with.common_data['pdb_chain'] == chain]
x_test = np.matrix(dataset[list(m_straight_with.common_data.columns)[1:-1]])
y_test = np.array(dataset[list(m_straight_with.common_data.columns)[-1]])
if np.sum(y_test==1) > 0:
fig.add_subplot(n,2, i+3-k)
data = m_straight_with.predict(x = x_test,
y = y_test,
model=m_straight_with.trained_model_validation)
plot = data['plots']['prob_density']
[eval(plot_string) for plot_string in plot]
#m_straight_with.show_plots(plot)
plt.title('Probabiity Distributions. %s\nPortion of sites - %.2f'%(chain.title(), np.sum(y_test==1)/y_test.shape[0]))
else:
print("Chain %s has no sites. "%(chain))
k += 1
Результаты на minresol (на которой тренировались).
In [13]:
fig = plt.figure(figsize = (20, 20))
fig.set_facecolor('white')
plt.subplots_adjust(hspace=0.3)
n = 3
k = 0
sss = StratifiedShuffleSplit(n_splits = 5, test_size = 0.3, random_state = 0)
split = sss.split(m_straight_without.x, m_straight_without.y)
for train_index, test_index in split:
x_test, y_test = m_straight_without.x[test_index], m_straight_without.y[test_index]
k += 1
fig.add_subplot(n,2, k)
data = m_straight_without.predict(x = x_test,
y = y_test,
model=m_straight_without.trained_model_validation)
plot = data['plots']['prob_density']
[eval(plot_string) for plot_string in plot]
plt.title('Probability Distributions. Split %d\nPortion of sites - %.2f'%(k, np.sum(y_test==1)/y_test.shape[0]))
k += 1
fig.add_subplot(n,2, k)
data = m_straight_without.predict(x = m_straight_without.x,
y = m_straight_without.y,
model=m_straight_without.trained_model_validation)
plot = data['plots']['prob_density']
[eval(plot_string) for plot_string in plot]
plt.title('Probability Distributions. Full dataset\nPortion of sites - %.2f'%(np.sum(y_test==1)/y_test.shape[0]));
Тренируемся на set_val.
In [20]:
fold = '../main_datasets/'
m_reverse_without = Magnesium_validation('../main_datasets/set_minresol_a_7_1000_new.csv', drop_common = True, file_ = "set_val_A_7_new.csv", fold = fold,
model = RandomForestClassifier(n_estimators=200, n_jobs=-1, criterion='gini', max_depth = 39, min_samples_leaf = 1))
In [21]:
m_reverse_without.train(n_splits=5);
Результаты на minresol, исключая совпадающие с трейном цепи.
In [31]:
fig = plt.figure(figsize = (20, 600))
fig.set_facecolor('white')
plt.subplots_adjust(hspace=0.7)
data_reverse_without = m_reverse_without.predict(x = m_reverse_without.x_test,
y = m_reverse_without.y_test,
model=m_reverse_without.trained_model_validation)
n = np.unique(m_reverse_without.validation_data['pdb_chain']).shape[0]//2+1
k = 0
fig.add_subplot(n,1, 1)
plot = data_reverse_without['plots']['prob_density']
[eval(plot_string) for plot_string in plot]
plt.title('Probabiity Distributions. Validation')
for i,chain in enumerate(np.unique(m_reverse_without.validation_data['pdb_chain'])):
dataset = m_reverse_without.validation_data[m_reverse_without.validation_data['pdb_chain'] == chain]
x_test = np.matrix(dataset[list(m_reverse_without.validation_data.columns)[1:-1]])
y_test = np.array(dataset[list(m_reverse_without.validation_data.columns)[-1]])
if np.sum(y_test==1) > 0:
fig.add_subplot(n,2, i+3-k)
data = m_reverse_without.predict(x = x_test,
y = y_test,
model=m_reverse_without.trained_model_validation)
plot = data['plots']['prob_density']
[eval(plot_string) for plot_string in plot]
plt.title('Probabiity Distributions. %s\nPortion of sites - %.2f'%(chain.title(), np.sum(y_test==1)/y_test.shape[0]))
else:
print("Chain %s has no sites. "%(chain))
k += 1
Результаты на minresol, исключая совпадающие с трейном цепи.
In [24]:
m_reverse_with = Magnesium_validation('../main_datasets/set_minresol_a_7_1000_new.csv', drop_common = False, file_ = "set_val_A_7_new.csv", fold = fold,
model = RandomForestClassifier(n_estimators=200, n_jobs=-1, criterion='gini', max_depth = 39, min_samples_leaf = 1))
m_reverse_with.trained_model_validation = m_reverse_without.trained_model_validation
fig = plt.figure(figsize = (20, 50))
fig.set_facecolor('white')
plt.subplots_adjust(hspace=0.7)
data_reverse_with = m_reverse_with.predict(x = m_reverse_with.x_test,
y = m_reverse_with.y_test,
model=m_reverse_with.trained_model_validation)
n = np.unique(m_reverse_with.common_data['pdb_chain']).shape[0]//2+2
k = 0
fig.add_subplot(n,1, 1)
plot = data_reverse_with['plots']['prob_density']
[eval(plot_string) for plot_string in plot]
plt.title('Probabiity Distributions. Validation \nPortion of sites - %.2f'%(np.sum(m_reverse_with.y_test==1)/m_reverse_with.y_test.shape[0]))
for i,chain in enumerate(np.unique(m_reverse_with.common_data['pdb_chain'])):
dataset = m_reverse_with.common_data[m_reverse_with.common_data['pdb_chain'] == chain]
x_test = np.matrix(dataset[list(m_reverse_with.common_data.columns)[1:-1]])
y_test = np.array(dataset[list(m_reverse_with.common_data.columns)[-1]])
if np.sum(y_test==1) > 0:
fig.add_subplot(n,2, i+3-k)
data = m_reverse_with.predict(x = x_test,
y = y_test,
model=m_reverse_with.trained_model_validation)
plot = data['plots']['prob_density']
[eval(plot_string) for plot_string in plot]
#m_reverse_with.show_plots(plot)
plt.title('Probabiity Distributions. %s\nPortion of sites - %.2f'%(chain.title(), np.sum(y_test==1)/y_test.shape[0]))
else:
print("Chain %s has no sites. "%(chain))
k += 1
Результаты на set_val (на которой тренировались).
In [35]:
fig = plt.figure(figsize = (20, 20))
fig.set_facecolor('white')
plt.subplots_adjust(hspace=0.3)
n = 3
k = 0
sss = StratifiedShuffleSplit(n_splits = 5, test_size = 0.3, random_state = 0)
split = sss.split(m_reverse_without.x, m_reverse_without.y)
for train_index, test_index in split:
x_test, y_test = m_reverse_without.x[test_index], m_reverse_without.y[test_index]
k += 1
fig.add_subplot(n,2, k)
data = m_reverse_without.predict(x = x_test,
y = y_test,
model=m_reverse_without.trained_model_validation)
plot = data['plots']['prob_density']
[eval(plot_string) for plot_string in plot]
plt.title('Probability Distributions. Split %d\nPortion of sites - %.2f'%(k, np.sum(y_test==1)/y_test.shape[0]))
k += 1
fig.add_subplot(n,2, k)
data = m_reverse_without.predict(x = m_reverse_without.x,
y = m_reverse_without.y,
model=m_reverse_without.trained_model_validation)
plot = data['plots']['prob_density']
[eval(plot_string) for plot_string in plot]
plt.title('Probability Distributions. Full dataset\nPortion of sites - %.2f'%(np.sum(y_test==1)/y_test.shape[0]));
Тренируемся на minresol, куда входят только цепочки длиной < 200
In [36]:
class Magnesium_validation(Magnesium):
def __init__(self, validation_file, drop_common = True, *args, **kwargs):
change_output('Loading data...')
super(Magnesium_validation, self).__init__(*args, **kwargs)
change_output('Loading validation data...')
self.validation_data = pd.read_table(validation_file).fillna(method = 'backfill', axis = 0)
if np.sum(self.validation_data.isnull().any(axis=1)) > 0:
self.validation_data.fillna(method = 'pad', axis = 0, inplace = True)
self.validation_data = self.validation_data[~(self.validation_data['chainlen']>1000)]
angles = ['p', 'phase-angle', 'e-z',
'tm', 'sszp', 'etap', 'etapp',
'splay', 'thetap', 'thetapp']
angles = np.ravel([[''.join([i,j]) for i in angles] for j in ['m2', 'm1', '', '1', '2']])
self.validation_data.drop(angles, axis=1)
self.data.drop(angles, axis=1)
if ('DSSR' in self.data.columns):
self.data.drop('DSSR', axis=1, inplace=True)
if ('DSSR' in self.validation_data.columns):
self.validation_data.drop('DSSR', axis=1, inplace=True)
change_output('Data loaded')
change_output('Data processing')
self.data = self.data[~self.data['pdb_chain'].isin(self.validation_data['pdb_chain'])]
self.data = self.data[self.data['chainlen']<200]
if drop_common:
self.validation_data = self.validation_data[~self.validation_data['pdb_chain'].isin(self.data['pdb_chain'])]
self.x_test = np.matrix(self.validation_data[list(self.validation_data.columns)[1:-1]])
self.y_test = np.array(self.validation_data[list(self.validation_data.columns)[-1]])
self.data_numpy = np.matrix(self.data)
self.x = self.data_numpy[:, 1:-1]
self.y = np.array(self.data_numpy[:,-1].flatten().tolist()[0])
change_output("Data processed")
def train(self, n_splits):
change_output("Start training...")
self.trained_model_validation = self.model
x = self.x
y = self.y
sss = StratifiedShuffleSplit(n_splits = n_splits, test_size = 0.3, random_state = 0)
rus = RandomUnderSampler(ratio = 'auto', random_state=42)
splitted = sss.split(x, y)
iterator = tqdm_notebook(splitted, desc = "Splits", leave = True) if tqdm else splitted
for train_index, test_index in iterator:
x_train, y_train = rus.fit_sample(x[train_index], y[train_index])
self.trained_model_validation.fit(x_train, y_train)
if not os.path.isdir('trained_models'):
os.mkdir('trained_models')
model_name = '%s_depth=%d_leaves=%d_%s_validation'%(re.split("\.|\'", str(self.trained_model_validation.__class__))[-2],
self.trained_model_validation.__dict__['max_depth'],
self.trained_model_validation.__dict__['min_samples_leaf'],
self.filename)
with open("trained_models/"+model_name+".sav", 'wb') as file_to_save:
pickle.dump(self.trained_model_validation, file_to_save)
change_output("Trained")
return [x[test_index], y[test_index]]
def compute_validated(self, n_splits = 3):
x_test, y_test = self.train(n_splits)
data = self.predict(x = self.x_test, y = self.y_test, model=self.trained_model_validation)
self.show_plots(data['plots'])
plt.text(0.02, 0.5, 'Predict', fontsize=14)
data_train = self.predict(x = x_test, y = y_test, model=self.trained_model_validation)
self.show_plots(data_train['plots'])
plt.text(0.02, 0.5, 'Train', fontsize=14)
self.validation_data['prediction'] = data['prediction']
self.validation_data['probability'] = data['probability']
return data
In [37]:
fold = '../main_datasets/'
m_chain_len = Magnesium_validation('../main_datasets/set_val_A_7_new.csv', drop_common = True, file_ = "set_minresol_a_7_1000_new.csv", fold = fold,
model = RandomForestClassifier(n_estimators=200, n_jobs=-1, criterion='gini', max_depth = 39, min_samples_leaf = 1))
In [39]:
m_chain_len.compute_validated(5);
